In WCS under configure access points check through your aps and see if you see one out of place. If you do delete it.

The only other option that comes to mind is to update to the latest WCS, which is 7.0.220.0. Ive been on 7.x WCS for about 9 months with no issues. And there is no issue with code compatibly. So long as your WCS is higher than your WLC you are good.

The upgrade should take you 30 - 60 minutes or so. Simply back up your WCS, unintsall old wcs, install new wcs, restore back up. Make sure you read the relase notes.

This behavior is by design. All you're doing removing an unassociated entry from WCS I don't see why it would create any other problem. In a long shot, even if you shut down WCS, it has no effect on your Wireless network/users/AP's.

If an AP goes offline/powered down/replaced, WCS would always hold the entry in it's local database so that it can update it's status once it's UP & operational but that seems to cause discrepancy when the reporting is done in the homepage. I'll check this internally.